Gastrointestinal tract

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Gastrointestinal_tract 

Gastrointestinal tract
Diagram of stomach, intestines and rectum in the average human
Details
System	Digestive system
Identifiers
Latin	Tractus digestorius (mouth to anus), canalis alimentarius (esophagus to large intestine), canalis gastrointestinales stomach to large intestine)
MeSH	D041981

The gastrointestinal tract, (GI tract, GIT, digestive tract, digestion tract, alimentary canal) is the tract from the mouth to the anus which includes all the organs of the digestive system in humans and other animals. Food taken in through the mouth is digested to extract nutrients and absorb energy, and the waste expelled as feces. The mouth, esophagus, stomach and intestines are all part of the gastrointestinal tract. Gastrointestinal is an adjective meaning of or pertaining to the stomach and intestines. A tract is a collection of related anatomic structures or a series of connected body organs.

All vertebrates and most invertebrates have a digestive tract. The sponges, cnidarians, and ctenophores are the early invertebrates with an incomplete digestive tract having just one opening instead of two, where food is taken in and waste expelled.

The human gastrointestinal tract consists of the esophagus, stomach, and intestines, and is divided into the upper and lower gastrointestinal tracts. The GI tract includes all structures between the mouth and the anus, forming a continuous passageway that includes the main organs of digestion, namely, the stomach, small intestine, and large intestine. However, the complete human digestive system is made up of the gastrointestinal tract plus the accessory organs of digestion (the tongue, salivary glands, pancreas, liver and gallbladder). The tract may also be divided into foregut, midgut, and hindgut, reflecting the embryological origin of each segment. The whole human GI tract is about nine metres (30 feet) long at autopsy. It is considerably shorter in the living body because the intestines, which are tubes of smooth muscle tissue, maintain constant muscle tone in a halfway-tense state but can relax in spots to allow for local distention and peristalsis.

The gastrointestinal tract contains trillions of microbes, with some 4,000 different strains of bacteria having diverse roles in maintenance of immune health and metabolism. Cells of the GI tract release hormones to help regulate the digestive process. These digestive hormones, including gastrin, secretin, cholecystokinin, and ghrelin, are mediated through either intracrine or autocrine mechanisms, indicating that the cells releasing these hormones are conserved structures throughout evolution.

Human gastrointestinal tract

Structure

Upper and lower human gastrointestinal tract

 

Illustration of human gastrointestinal tract

The structure and function can be described both as gross anatomy and as microscopic anatomy or histology. The tract itself is divided into upper and lower tracts, and the intestines small and large parts.

Upper gastrointestinal tract

The upper gastrointestinal tract consists of the mouth, pharynx, esophagus, stomach, and duodenum. The exact demarcation between the upper and lower tracts is the suspensory muscle of the duodenum. This differentiates the embryonic borders between the foregut and midgut, and is also the division commonly used by clinicians to describe gastrointestinal bleeding as being of either "upper" or "lower" origin. Upon dissection, the duodenum may appear to be a unified organ, but it is divided into four segments based upon function, location, and internal anatomy. The four segments of the duodenum are as follows (starting at the stomach, and moving toward the jejunum): bulb, descending, horizontal, and ascending. The suspensory muscle attaches the superior border of the ascending duodenum to the diaphragm.

The suspensory muscle is an important anatomical landmark which shows the formal division between the duodenum and the jejunum, the first and second parts of the small intestine, respectively. This is a thin muscle which is derived from the embryonic mesoderm.

Lower gastrointestinal tract

The lower gastrointestinal tract includes most of the small intestine and all of the large intestine. In human anatomy, the intestine (bowel, or gut. Greek: éntera) is the segment of the gastrointestinal tract extending from the pyloric sphincter of the stomach to the anus and as in other mammals, consists of two segments, the small intestine and the large intestine. In humans, the small intestine is further subdivided into the duodenum, jejunum and ileum while the large intestine is subdivided into the cecum, ascending, transverse, descending and sigmoid colon, rectum, and anal canal.

Small intestine

The small intestine begins at the duodenum and is a tubular structure, usually between 6 and 7 m long. Its mucosal area in an adult human is about 30 m² (320 sq ft). The combination of the circular folds, the villi, and the microvilli increases the absorptive area of the mucosa about 600-fold, making a total area of about 250 m² (2,700 sq ft) for the entire small intestine. Its main function is to absorb the products of digestion (including carbohydrates, proteins, lipids, and vitamins) into the bloodstream. There are three major divisions:

1. Duodenum: A short structure (about 20–25 cm long) which receives chyme from the stomach, together with pancreatic juice containing digestive enzymes and bile from the gall bladder. The digestive enzymes break down proteins, and bile emulsifies fats into micelles. The duodenum contains Brunner's glands which produce a mucus-rich alkaline secretion containing bicarbonate. These secretions, in combination with bicarbonate from the pancreas, neutralize the stomach acids contained in the chyme.
2. Jejunum: This is the midsection of the small intestine, connecting the duodenum to the ileum. It is about 2.5 m (8.2 ft) long and contains the circular folds also known as plicae circulares and villi that increase its surface area. Products of digestion (sugars, amino acids, and fatty acids) are absorbed into the bloodstream here.
3. Ileum: The final section of the small intestine. It is about 3 m long, and contains villi similar to the jejunum. It absorbs mainly vitamin B12 and bile acids, as well as any other remaining nutrients.

Large intestine

The large intestine also called the colon, consists of the cecum, rectum, and anal canal. It also includes the appendix, which is attached to the cecum. The colon is further divided into:

1. Cecum (first portion of the colon) and appendix
2. Ascending colon (ascending in the back wall of the abdomen)
3. Right colic flexure (flexed portion of the ascending and transverse colon apparent to the liver)
4. Transverse colon (passing below the diaphragm)
5. Left colic flexure (flexed portion of the transverse and descending colon apparent to the spleen)
6. Descending colon (descending down the left side of the abdomen)
7. Sigmoid colon (a loop of the colon closest to the rectum)
8. Rectum
9. Anus

The main function of the large intestine is to absorb water. The area of the large intestinal mucosa of an adult human is about 2 m² (22 sq ft).

Development

The gut is an endoderm-derived structure. At approximately the sixteenth day of human development, the embryo begins to fold ventrally (with the embryo's ventral surface becoming concave) in two directions: the sides of the embryo fold in on each other and the head and tail fold toward one another. The result is that a piece of the yolk sac, an endoderm-lined structure in contact with the ventral aspect of the embryo, begins to be pinched off to become the primitive gut. The yolk sac remains connected to the gut tube via the vitelline duct. Usually, this structure regresses during development; in cases where it does not, it is known as Meckel's diverticulum.

During fetal life, the primitive gut is gradually patterned into three segments: foregut, midgut, and hindgut. Although these terms are often used in reference to segments of the primitive gut, they are also used regularly to describe regions of the definitive gut as well.

Each segment of the gut is further specified and gives rise to specific gut and gut-related structures in later development. Components derived from the gut proper, including the stomach and colon, develop as swellings or dilatations in the cells of the primitive gut. In contrast, gut-related derivatives — that is, those structures that derive from the primitive gut but are not part of the gut proper, in general, develop as out-pouchings of the primitive gut. The blood vessels supplying these structures remain constant throughout development.

Part	Part in adult	Gives rise to	Arterial supply
Foregut	esophagus to first 2 sections of the duodenum	Esophagus, stomach, duodenum (1st and 2nd parts), liver, gallbladder, pancreas, superior portion of pancreas (Note that though the spleen is supplied by the celiac trunk, it is derived from dorsal mesentery and therefore not a foregut derivative)	celiac trunk
Midgut	lower duodenum, to the first two-thirds of the transverse colon	lower duodenum, jejunum, ileum, cecum, appendix, ascending colon, and first two-thirds of the transverse colon	branches of the superior mesenteric artery
Hindgut	last third of the transverse colon, to the upper part of the anal canal	last third of the transverse colon, descending colon, rectum, and upper part of the anal canal	branches of the inferior mesenteric artery

Histology

General structure of the gut wall

• 1: Mucosa: Epithelium
• 2: Mucosa: Lamina propria
• 3: Mucosa: Muscularis mucosae
• 4: Lumen
• 5: Lymphatic tissue
• 6: Duct of gland outside tract
• 7: Gland in mucosa
• 8: Submucosa
• 9: Glands in submucosa
• 10: Meissner's submucosal plexus
• 11: Vein
• 12: Muscularis: Circular muscle
• 13: Muscularis: Longitudinal muscle
• 14: Serosa: Areolar connective tissue
• 15: Serosa: Epithelium
• 16: Auerbach's myenteric plexus
• 17: Nerve
• 18: Artery
• 19: Mesentery

The gastrointestinal tract has a form of general histology with some differences that reflect the specialization in functional anatomy. The GI tract can be divided into four concentric layers in the following order:

• Mucosa
• Submucosa
• Muscular layer
• Adventitia or serosa

Mucosa

The mucosa is the innermost layer of the gastrointestinal tract. The mucosa surrounds the lumen, or open space within the tube. This layer comes in direct contact with digested food (chyme). The mucosa is made up of:

• Epithelium – innermost layer. Responsible for most digestive, absorptive and secretory processes.
• Lamina propria – a layer of connective tissue. Unusually cellular compared to most connective tissue
• Muscularis mucosae – a thin layer of smooth muscle that aids the passing of material and enhances the interaction between the epithelial layer and the contents of the lumen by agitation and peristalsis

The mucosae are highly specialized in each organ of the gastrointestinal tract to deal with the different conditions. The most variation is seen in the epithelium.

Submucosa

The submucosa consists of a dense irregular layer of connective tissue with large blood vessels, lymphatics, and nerves branching into the mucosa and muscularis externa. It contains the submucosal plexus, an enteric nervous plexus, situated on the inner surface of the muscularis externa.

Muscular layer

The muscular layer consists of an inner circular layer and a longitudinal outer layer. The circular layer prevents food from traveling backward and the longitudinal layer shortens the tract. The layers are not truly longitudinal or circular, rather the layers of muscle are helical with different pitches. The inner circular is helical with a steep pitch and the outer longitudinal is helical with a much shallower pitch. Whilst the muscularis externa is similar throughout the entire gastrointestinal tract, an exception is the stomach which has an additional inner oblique muscular layer to aid with grinding and mixing of food. The muscularis externa of the stomach is composed of the inner oblique layer, middle circular layer, and outer longitudinal layer.

Between the circular and longitudinal muscle layers is the myenteric plexus. This controls peristalsis. Activity is initiated by the pacemaker cells, (myenteric interstitial cells of Cajal). The gut has intrinsic peristaltic activity (basal electrical rhythm) due to its self-contained enteric nervous system. The rate can be modulated by the rest of the autonomic nervous system.

The coordinated contractions of these layers is called peristalsis and propels the food through the tract. Food in the GI tract is called a bolus (ball of food) from the mouth down to the stomach. After the stomach, the food is partially digested and semi-liquid, and is referred to as chyme. In the large intestine the remaining semi-solid substance is referred to as faeces.

Adventitia and serosa

The outermost layer of the gastrointestinal tract consists of several layers of connective tissue.

Intraperitoneal parts of the GI tract are covered with serosa. These include most of the stomach, first part of the duodenum, all of the small intestine, caecum and appendix, transverse colon, sigmoid colon and rectum. In these sections of the gut, there is a clear boundary between the gut and the surrounding tissue. These parts of the tract have a mesentery.

Retroperitoneal parts are covered with adventitia. They blend into the surrounding tissue and are fixed in position. For example, the retroperitoneal section of the duodenum usually passes through the transpyloric plane. These include the esophagus, pylorus of the stomach, distal duodenum, ascending colon, descending colon and anal canal. In addition, the oral cavity has adventitia.

Gene and protein expression

Approximately 20,000 protein coding genes are expressed in human cells and 75% of these genes are expressed in at least one of the different parts of the digestive organ system. Over 600 of these genes are more specifically expressed in one or more parts of the GI tract and the corresponding proteins have functions related to digestion of food and uptake of nutrients. Examples of specific proteins with such functions are pepsinogen PGC and the lipase LIPF, expressed in chief cells, and gastric ATPase ATP4A and gastric intrinsic factor GIF, expressed in parietal cells of the stomach mucosa. Specific proteins expressed in the stomach and duodenum involved in defence include mucin proteins, such as mucin 6 and intelectin-1.

Time taken

The time taken for food to transit through the gastrointestinal tract varies on multiple factors, including age, ethnicity, and gender. Several techniques have been used to measure transit time, including radiography following a barium-labeled meal, breath hydrogen analysis, and scintigraphic analysis following a radiolabeled meal. It takes 2.5 to 3 hours for 50% of the contents to leave the stomach. The rate of digestion is also dependent of the material being digested, as food composition from the same meal may leave the stomach at different rates. Total emptying of the stomach takes around 4–5 hours, and transit through the colon takes 30 to 50 hours.

Immune function

The gastrointestinal tract forms an important part of the immune system.

Immune barrier

The surface area of the digestive tract is estimated to be about 32 square meters, or about half a badminton court. With such a large exposure (more than three times larger than the exposed surface of the skin), these immune components function to prevent pathogens from entering the blood and lymph circulatory systems. Fundamental components of this protection are provided by the intestinal mucosal barrier, which is composed of physical, biochemical, and immune elements elaborated by the intestinal mucosa. Microorganisms also are kept at bay by an extensive immune system comprising the gut-associated lymphoid tissue (GALT)

There are additional factors contributing to protection from pathogen invasion. For example, low pH (ranging from 1 to 4) of the stomach is fatal for many microorganisms that enter it. Similarly, mucus (containing IgA antibodies) neutralizes many pathogenic microorganisms. Other factors in the GI tract contribution to immune function include enzymes secreted in the saliva and bile.

Immune system homeostasis

Beneficial bacteria also can contribute to the homeostasis of the gastrointestinal immune system. For example, Clostridia, one of the most predominant bacterial groups in the GI tract, play an important role in influencing the dynamics of the gut's immune system. It has been demonstrated that the intake of a high fiber diet could be responsible for the induction of T-regulatory cells (Tregs). This is due to the production of short-chain fatty acids during the fermentation of plant-derived nutrients such as butyrate and propionate. Basically, the butyrate induces the differentiation of Treg cells by enhancing histone H3 acetylation in the promoter and conserved non-coding sequence regions of the FOXP3 locus, thus regulating the T cells, resulting in the reduction of the inflammatory response and allergies.

Intestinal microbiota

The large intestine hosts several kinds of bacteria that can deal with molecules that the human body cannot otherwise break down. This is an example of symbiosis. These bacteria also account for the production of gases at host-pathogen interface, inside our intestine (this gas is released as flatulence when eliminated through the anus). However the large intestine is mainly concerned with the absorption of water from digested material (which is regulated by the hypothalamus) and the re absorption of sodium, as well as any nutrients that may have escaped primary digestion in the ileum.

Health-enhancing intestinal bacteria of the gut flora serve to prevent the overgrowth of potentially harmful bacteria in the gut. These two types of bacteria compete for space and "food", as there are limited resources within the intestinal tract. A ratio of 80-85% beneficial to 15–20% potentially harmful bacteria generally is considered normal within the intestines.

Detoxification and drug metabolism

Enzymes such as CYP3A4, along with the antiporter activities, are also instrumental in the intestine's role of drug metabolism in the detoxification of antigens and xenobiotics.

Clinical significance

This section discusses related diseases, medical associations with the gastrointestinal tract, and use in surgery.

Diseases

There are many diseases and conditions that can affect the gastrointestinal system, including infections, inflammation and cancer.

Various pathogens, such as bacteria that cause foodborne illnesses, can induce gastroenteritis which results from inflammation of the stomach and small intestine. Antibiotics to treat such bacterial infections can decrease the microbiome diversity of the gastrointestinal tract, and further enable inflammatory mediators. Gastroenteritis is the most common disease of the GI tract.

• Gastrointestinal cancer may occur at any point in the gastrointestinal tract, and includes mouth cancer, tongue cancer, oesophageal cancer, stomach cancer, and colorectal cancer.
• Inflammatory conditions. Ileitis is an inflammation of the ileum, colitis is an inflammation of the large intestine.
• Appendicitis is inflammation of the appendix located at the caecum. This is a potentially fatal condition if left untreated; most cases of appendicitis require surgical intervention.

Diverticular disease is a condition that is very common in older people in industrialized countries. It usually affects the large intestine but has been known to affect the small intestine as well. Diverticulosis occurs when pouches form on the intestinal wall. Once the pouches become inflamed it is known as diverticulitis.

Inflammatory bowel disease is an inflammatory condition affecting the bowel walls, and includes the subtypes Crohn's disease and ulcerative colitis. While Crohn's can affect the entire gastrointestinal tract, ulcerative colitis is limited to the large intestine. Crohn's disease is widely regarded as an autoimmune disease. Although ulcerative colitis is often treated as though it were an autoimmune disease, there is no consensus that it actually is such.

Functional gastrointestinal disorders the most common of which is irritable bowel syndrome. Functional constipation and chronic functional abdominal pain are other functional disorders of the intestine that have physiological causes but do not have identifiable structural, chemical, or infectious pathologies.

Symptoms

Several symptoms are used to indicate problems with the gastrointestinal tract:

• Vomiting, which may include regurgitation of food or the vomiting of blood
• Diarrhea, or the passage of liquid or more frequent stools
• Constipation, which refers to the passage of fewer and hardened stools
• Blood in stool, which includes fresh red blood, maroon-coloured blood, and tarry-coloured blood

Treatment

Gastrointestinal surgery can often be performed in the outpatient setting. In the United States in 2012, operations on the digestive system accounted for 3 of the 25 most common ambulatory surgery procedures and constituted 9.1 percent of all outpatient ambulatory surgeries.

Imaging

Various methods of imaging the gastrointestinal tract include the upper and lower gastrointestinal series:

• Radioopaque dyes may be swallowed to produce a barium swallow
• Parts of the tract may be visualised by camera. This is known as endoscopy if examining the upper gastrointestinal tract and colonoscopy or sigmoidoscopy if examining the lower gastrointestinal tract. Capsule endoscopy is where a capsule containing a camera is swallowed in order to examine the tract. Biopsies may also be taken when examined.
• An abdominal x-ray may be used to examine the lower gastrointestinal tract.

Other related diseases

• Cholera
• Enteric duplication cyst
• Giardiasis
• Pancreatitis
• Peptic ulcer disease
• Yellow fever
• Helicobacter pylori is a gram-negative spiral bacterium. Over half the world's population is infected with it, mainly during childhood; it is not certain how the disease is transmitted. It colonizes the gastrointestinal system, predominantly the stomach. The bacterium has specific survival conditions that our gastric microenvironment: it is both capnophilic and microaerophilic. Helicobacter also exhibits a tropism for gastric epithelial lining and the gastric mucosal layer about it. Gastric colonization of this bacterium triggers a robust immune response leading to moderate to severe inflammation, known as gastritis. Signs and symptoms of infection are gastritis, burning abdominal pain, weight loss, loss of appetite, bloating, burping, nausea, bloody vomit, and black tarry stools. Infection can be detected in a number of ways: GI X-rays, endoscopy, blood tests for anti-Helicobacter antibodies, a stool test, and a urease breath test (which is a by-product of the bacteria). If caught soon enough, it can be treated with three doses of different proton pump inhibitors as well as two antibiotics, taking about a week to cure. If not caught soon enough, surgery may be required.
• Intestinal pseudo-obstruction is a syndrome caused by a malformation of the digestive system, characterized by a severe impairment in the ability of the intestines to push and assimilate. Symptoms include daily abdominal and stomach pain, nausea, severe distension, vomiting, heartburn, dysphagia, diarrhea, constipation, dehydration and malnutrition. There is no cure for intestinal pseudo-obstruction. Different types of surgery and treatment managing life-threatening complications such as ileus and volvulus, intestinal stasis which lead to bacterial overgrowth, and resection of affected or dead parts of the gut may be needed. Many patients require parenteral nutrition.
• Ileus is a blockage of the intestines.
• Coeliac disease is a common form of malabsorption, affecting up to 1% of people of northern European descent. An autoimmune response is triggered in intestinal cells by digestion of gluten proteins. Ingestion of proteins found in wheat, barley and rye, causes villous atrophy in the small intestine. Lifelong dietary avoidance of these foodstuffs in a gluten-free diet is the only treatment.
• Enteroviruses are named by their transmission-route through the intestine (enteric meaning intestinal), but their symptoms aren't mainly associated with the intestine.
• Endometriosis can affect the intestines, with similar symptoms to IBS.
• Bowel twist (or similarly, bowel strangulation) is a comparatively rare event (usually developing sometime after major bowel surgery). It is, however, hard to diagnose correctly, and if left uncorrected can lead to bowel infarction and death. (The singer Maurice Gibb is understood to have died from this.)
• Angiodysplasia of the colon
• Constipation
• Diarrhea
• Hirschsprung's disease (aganglionosis)
• Intussusception
• Polyp (medicine) (see also colorectal polyp)
• Pseudomembranous colitis
• Toxic megacolon usually a complication of ulcerative colitis

Uses of animal guts

Intestines from animals other than humans are used in a number of ways. From each species of livestock that is a source of milk, a corresponding rennet is obtained from the intestines of milk-fed calves. Pig and calf intestines are eaten, and pig intestines are used as sausage casings. Calf intestines supply calf-intestinal alkaline phosphatase (CIP), and are used to make goldbeater's skin. Other uses are:

• The use of animal gut strings by musicians can be traced back to the third dynasty of Egypt. In the recent past, strings were made out of lamb gut. With the advent of the modern era, musicians have tended to use strings made of silk, or synthetic materials such as nylon or steel. Some instrumentalists, however, still use gut strings in order to evoke the older tone quality. Although such strings were commonly referred to as "catgut" strings, cats were never used as a source for gut strings.
• Sheep gut was the original source for natural gut string used in racquets, such as for tennis. Today, synthetic strings are much more common, but the best gut strings are now made out of cow gut.
• Gut cord has also been used to produce strings for the snares that provide a snare drum's characteristic buzzing timbre. While the modern snare drum almost always uses metal wire rather than gut cord, the North African bendir frame drum still uses gut for this purpose.
• "Natural" sausage hulls, or casings, are made of animal gut, especially hog, beef, and lamb.
• The wrapping of kokoretsi, gardoubakia, and torcinello is made of lamb (or goat) gut.
• Haggis is traditionally boiled in, and served in, a sheep stomach.
• Chitterlings, a kind of food, consist of thoroughly washed pig's gut.
• Animal gut was used to make the cord lines in longcase clocks and for fusee movements in bracket clocks, but may be replaced by metal wire.
• The oldest known condoms, from 1640 AD, were made from animal intestine.

Other animals

Many birds and other animals have a specialised stomach in the digestive tract called a gizzard used for grinding up food.

Another feature not found in the human but found in a range of other animals is the crop. In birds this is found as a pouch alongside the esophagus.

Other animals including amphibians, birds, reptiles, and egg-laying mammals have a major difference in their GI tract in that it ends in a cloaca and not an anus.

In 2020, the oldest known fossil digestive tract, of an extinct wormlike organism in the Cloudinidae was discovered; it lived during the late Ediacaran period about 550 million years ago.

Adaptive evolution in the human genome

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Adaptive_evolution_in_the_human_genome 

Adaptive evolution results from the propagation of advantageous mutations through positive selection. This is the modern synthesis of the process which Darwin and Wallace originally identified as the mechanism of evolution. However, in the last half century there has been considerable debate as to whether evolutionary changes at the molecular level are largely driven by natural selection or random genetic drift. Unsurprisingly, the forces which drive evolutionary changes in our own species’ lineage have been of particular interest. Quantifying adaptive evolution in the human genome gives insights into our own evolutionary history and helps to resolve this neutralist-selectionist debate. Identifying specific regions of the human genome that show evidence of adaptive evolution helps us find functionally significant genes, including genes important for human health, such as those associated with diseases.

Methods

The methods used to identify adaptive evolution are generally devised to test the null hypothesis of neutral evolution, which, if rejected, provides evidence of adaptive evolution. These tests can be broadly divided into two categories.

Firstly, there are methods that use a comparative approach to search for evidence of function altering mutations. The dN/dS rates-ratio test estimates ω, the rates at which nonsynonymous ('dN') and synonymous ('dS') nucleotide substitutions occur ('synonymous' nucleotide substitutions do not lead to a change in the coding amino acid, while 'nonsynonymous' ones do). In this model, neutral evolution is considered the null hypothesis, in which dN and dS approximately balance so that ω ≈ 1. The two alternative hypotheses are a relative absence of nonsynonymous substitutions (dN < dS; ω < 1), suggesting the effect on fitness ('fitness effect', or 'selection pressure') of such mutations is negative (purifying selection has operated over time); or a relative excess of nonsynonymous substitutions (dN > dS; ω > 1), indicating positive effect on fitness, i.e. diversifying selection (Yang and Bielawski 2000).

The McDonald-Kreitman (MK) test quantifies the amount of adaptive evolution occurring by estimating the proportion of nonsynonymous substitutions which are adaptive, referred to as α (McDonald and Kreitman 1991, Eyre-Walker 2006). α is calculated as: α = 1-(dspn/dnps), where dn and ds are as above, and pn and ps are the number of nonsynonymous (fitness effect assumed neutral or deleterious) and synonymous (fitness effect assumed neutral) polymorphisms respectively (Eyre-Walker 2006).

Note, both these tests are presented here in basic forms, and these tests are normally modified considerably to account for other factors, such as the effect of slightly deleterious mutations.

The other methods for detecting adaptive evolution use genome wide approaches, often to look for evidence of selective sweeps. Evidence of complete selective sweeps is shown by a decrease in genetic diversity, and can be inferred from comparing the patterns of the Site Frequency Spectrum (SFS, i.e. the allele frequency distribution) obtained with the SFS expected under a neutral model (Willamson et al. 2007). Partial selective sweeps provide evidence of the most recent adaptive evolution, and the methods identify adaptive evolution by searching for regions with a high proportion of derived alleles (Sabeti et al. 2006).

Examining patterns of Linkage Disequilibrium (LD) can locate signatures of adaptive evolution (Hawks et al. 2007, Voight et al. 2006). LD tests work on the basic principle that, assuming equal recombination rates, LD will rise with increasing natural selection. These genomic methods can also be applied to search for adaptive evolution in non-coding DNA, where putatively neutral sites are hard to identify (Ponting and Lunter 2006).

Another recent method used to detect selection in non-coding sequences examines insertions and deletions (indels), rather than point mutations (Lunter et al. 2006), although the method has only been applied to examine patterns of negative selection.

Amount of adaptive evolution

Coding DNA

Many different studies have attempted to quantify the amount of adaptive evolution in the human genome, the vast majority using the comparative approaches outlined above. Although there are discrepancies between studies, generally there is relatively little evidence of adaptive evolution in protein coding DNA, with estimates of adaptive evolution often near 0% (see Table 1). The most obvious exception to this is the 35% estimate of α (Fay et al. 2001). This comparatively early study used relatively few loci (fewer than 200) for their estimate, and the polymorphism and divergence data used was obtained from different genes, both of which may have led to an overestimate of α. The next highest estimate is the 20% value of α (Zhang and Li 2005). However, the MK test used in this study was sufficiently weak that the authors state that this value of α is not statistically significantly different from 0%. Nielsen et al. (2005a)’s estimate that 9.8% of genes have undergone adaptive evolution also has a large margin of error associated with it, and their estimate shrinks dramatically to 0.4% when they stipulate that the degree of certainty that there has been adaptive evolution must be 95% or more.

This raises an important issue, which is that many of these tests for adaptive evolution are very weak. Therefore, the fact that many estimates are at (or very near to) 0% does not rule out the occurrence of any adaptive evolution in the human genome, but simply shows that positive selection is not frequent enough to be detected by the tests. In fact, the most recent study mentioned states that confounding variables, such as demographic changes, mean that the true value of α may be as high as 40% (Eyre-Walker and Keightley 2009). Another recent study, which uses a relatively robust methodology, estimates α at 10-20% Boyko et al. (2008). Clearly, the debate over the amount of adaptive evolution occurring in human coding DNA is not yet resolved.

Even if low estimates of α are accurate, a small proportion of substitutions evolving adaptively can still equate to a considerable amount of coding DNA. Many authors, whose studies have small estimates of the amount of adaptive evolution in coding DNA, nevertheless accept that there has been some adaptive evolution in this DNA, because these studies identify specific regions within the human genome which have been evolving adaptively (e.g. Bakewell et al. (2007)). More genes underwent positive selection in chimpanzee evolution than in human.

The generally low estimates of adaptive evolution in human coding DNA can be contrasted with other species. Bakewell et al. (2007) found more evidence of adaptive evolution in chimpanzees than humans, with 1.7% of chimpanzee genes showing evidence of adaptive evolution (compared with the 1.1% estimate for humans; see Table 1). Comparing humans with more distantly related animals, an early estimate for α in Drosophila species was 45% (Smith and Eyre-Walker 2002), and later estimates largely agree with this (Eyre-Walker 2006). Bacteria and viruses generally show even more evidence of adaptive evolution; research shows values of α in a range of 50-85%, depending on the species examined (Eyre-Walker 2006). Generally, there does appear to be a positive correlation between (effective) population size of the species, and amount of adaptive evolution occurring in the coding DNA regions. This may be because random genetic drift becomes less powerful at altering allele frequencies, compared to natural selection, as population size increases.

Non-coding DNA

Estimates of the amount of adaptive evolution in non-coding DNA are generally very low, although fewer studies have been done on non-coding DNA. As with the coding DNA however, the methods currently used are relatively weak. Ponting and Lunter (2006) speculate that underestimates may be even more severe in non-coding DNA, because non-coding DNA may undergo periods of functionality (and adaptive evolution), followed by periods of neutrality. If this is true, current methods for detecting adaptive evolution are inadequate to account for such patterns. Additionally, even if low estimates of the amount of adaptive evolution are correct, this can still equate to a large amount of adaptively evolving non-coding DNA, since non-coding DNA makes up approximately 98% of the DNA in the human genome. For example, Ponting and Lunter (2006) detect a modest 0.03% of non-coding DNA showing evidence of adaptive evolution, but this still equates to approximately 1 Mb of adaptively evolving DNA. Where there is evidence of adaptive evolution (which implies functionality) in non-coding DNA, these regions are generally thought to be involved in the regulation of protein coding sequences.

As with humans, fewer studies have searched for adaptive evolution in non-coding regions of other organisms. However, where research has been done on Drosophila, there appears to be large amounts of adaptively evolving non-coding DNA. Andolfatto (2005) estimated that adaptive evolution has occurred in 60% of untranslated mature portions of mRNAs, and in 20% of intronic and intergenic regions. If this is true, this would imply that much non-coding DNA could be of more functional importance than coding DNA, dramatically altering the consensus view. However, this would still leave unanswered what function all this non-coding DNA performs, as the regulatory activity observed thus far is in just a tiny proportion of the total amount of non-coding DNA. Ultimately, significantly more evidence needs to be gathered to substantiate this viewpoint.

Variation between human populations

Several recent studies have compared the amounts of adaptive evolution occurring between different populations within the human species. Williamson et al. (2007) found more evidence of adaptive evolution in European and Asian populations than African American populations. Assuming African Americans are representative of Africans, these results makes sense intuitively, because humans spread out of Africa approximately 50,000 years ago (according to the consensus Out-of-Africa hypothesis of human origins (Klein 2009)), and these humans would have adapted to the new environments they encountered. By contrast, African populations remained in a similar environment for the following tens of thousands of years, and were therefore probably nearer their adaptive peak for the environment. However, Voight et al. (2006) found evidence of more adaptive evolution in Africans, than in Non-Africans (East Asian and European populations examined), and Boyko et al. (2008) found no significant difference in the amount of adaptive evolution occurring between different human populations. Therefore, the evidence obtained so far is inconclusive as to what extent different human populations have undergone different amounts of adaptive evolution.

Rate of adaptive evolution

The rate of adaptive evolution in the human genome has often been assumed to be constant over time. For example, the 35% estimate for α calculated by Fay et al. (2001) led them to conclude that there was one adaptive substitution in the human lineage every 200 years since human divergence from old-world monkeys. However, even if the original value of α is accurate for a particular time period, this extrapolation is still invalid. This is because there has been a large acceleration in the amount of positive selection in the human lineage over the last 40,000 years, in terms of the number of genes that have undergone adaptive evolution (Hawks et al. 2007). This agrees with simple theoretical predictions, because the human population size has expanded dramatically in the last 40,000 years, and with more people, there should be more adaptive substitutions. Hawks et al. (2007) argue that demographic changes (particularly population expansion) may greatly facilitate adaptive evolution, an argument that somewhat corroborates the positive correlation inferred between population size and amount of adaptive evolution occurring mentioned previously.

It has been suggested that cultural evolution may have replaced genetic evolution, and hence slowed the rate of adaptive evolution over the past 10,000 years. However, it is possible that cultural evolution could actually increase genetic adaption. Cultural evolution has vastly increased communication and contact between different populations, and this provides much greater opportunities for genetic admixture between the different populations (Hawks et al. 2007). However, recent cultural phenomena, such as modern medicine and the smaller variation in modern family sizes, may reduce genetic adaption as natural selection is relaxed, overriding the increased potential for adaptation due to greater genetic admixture.

Strength of positive selection

Studies generally do not attempt to quantify the average strength of selection propagating advantageous mutations in the human genome. Many models make assumptions about how strong selection is, and some of the discrepancies between the estimates of the amounts of adaptive evolution occurring have been attributed to the use of such differing assumptions (Eyre-Walker 2006). The way to accurately estimate the average strength of positive selection acting on the human genome is by inferring the distribution of fitness effects (DFE) of new advantageous mutations in the human genome, but this DFE is difficult to infer because new advantageous mutations are very rare (Boyko et al. 2008). The DFE may be exponential shaped in an adapted population (Eyre-Walker and Keightley 2007). However, more research is required to produce more accurate estimates of the average strength of positive selection in humans, which will in turn improve the estimates of the amount of adaptive evolution occurring in the human genome (Boyko et al. 2008).

Regions of the genome which show evidence of adaptive evolution

A considerable number of studies have used genomic methods to identify specific human genes that show evidence of adaptive evolution. Table 2 gives selected examples of such genes for each gene type discussed, but provides nowhere near an exhaustive list of the human genes showing evidence of adaptive evolution. Below are listed some of the types of gene which show strong evidence of adaptive evolution in the human genome.

• Disease genes

Bakewell et al. (2007) found that a relatively large proportion (9.7%) of positively selected genes were associated with diseases. This may be because diseases can be adaptive in some contexts. For example, schizophrenia has been linked with increased creativity (Crespi et al. 2007), perhaps a useful trait for obtaining food or attracting mates in Palaeolithic times. Alternatively, the adaptive mutations may be the ones which reduce the chance of disease arising due to other mutations. However, this second explanation seems unlikely, because the mutation rate in the human genome is fairly low, so selection would be relatively weak.

• Immune genes

417 genes involved in the immune system showed strong evidence of adaptive evolution in the study of Nielsen et al. (2005a). This is probably because the immune genes may become involved in an evolutionary arms race with bacteria and viruses (Daugherty and Malik 2012; Van der Lee et al. 2017). These pathogens evolve very rapidly, so selection pressures change quickly, giving more opportunity for adaptive evolution.

• Testes genes

247 genes in the testes showed evidence of adaptive evolution in the study of Nielsen et al. (2005a). This could be partially due to sexual antagonism. Male-female competition could facilitate an arms race of adaptive evolution. However, in this situation you would expect to find evidence of adaptive evolution in the female sexual organs also, but there is less evidence of this. Sperm competition is another possible explanation. Sperm competition is strong, and sperm can improve their chances of fertilising the female egg in a variety of ways, including increasing their speed, stamina or response to chemoattractants (Swanson and Vacquier 2002).

• Olfactory genes

Genes involved in detecting smell show strong evidence of adaptive evolution (Voight et al. 2006), probably due to the fact that the smells encountered by humans have changed recently in their evolutionary history (Williamson et al. 2007). Humans’ sense of smell has played an important role in determining the safety of food sources.

• Nutrition genes

Genes involved in lactose metabolism show particularly strong evidence of adaptive evolution amongst the genes involved in nutrition. A mutation linked to lactase persistence shows very strong evidence of adaptive evolution in European and American populations (Williamson et al. 2007), populations where pastoral farming for milk has been historically important.

• Pigmentation genes

Pigmentation genes show particularly strong evidence of adaptive evolution in non-African populations (Williamson et al. 2007). This is likely to be because those humans that left Africa approximately 50,000 years ago, entered less sunny climates, and so were under new selection pressures to obtain enough Vitamin D from the weakened sunlight.

• Brain genes?

There is some evidence of adaptive evolution in genes linked to brain development, but some of these genes are often associated with diseases, e.g. microcephaly (see Table 2). However, there is a particular interest in the search for adaptive evolution in brain genes, despite the ethical issues surrounding such research. If more adaptive evolution was discovered in brain genes in one human population than another, then this information could be interpreted as showing greater intelligence in the more adaptively evolved population.

• Other

Other gene types showing considerable evidence of adaptive evolution (but generally less evidence than the types discussed) include: genes on the X chromosome, nervous system genes, genes involved in apoptosis, genes coding for skeletal traits, and possibly genes associated with speech (Nielsen et al. 2005a, Williamson et al. 2007, Voight et al. 2006, Krause et al. 2007).

Difficulties in identifying positive selection

As noted previously, many of the tests used to detect adaptive evolution have very large degrees of uncertainty surrounding their estimates. While there are many different modifications applied to individual tests to overcome the associated problems, two types of confounding variables are particularly important in hindering the accurate detection of adaptive evolution: demographic changes and biased gene conversion.

Demographic changes are particularly problematic and may severely bias estimates of adaptive evolution. The human lineage has undergone both rapid population size contractions and expansions over its evolutionary history, and these events will change many of the signatures thought to be characteristic of adaptive evolution (Nielsen et al. 2007). Some genomic methods have been shown through simulations to be relatively robust to demographic changes (e.g. Willamson et al. 2007). However, no tests are completely robust to demographic changes, and new genetic phenomena linked to demographic changes have recently been discovered. This includes the concept of “surfing mutations”, where new mutations can be propagated with a population expansion (Klopfstein et al. 2006).

A phenomenon which could severely alter the way we look for signatures of adaptive evolution is biased gene conversion (BGC) (Galtier and Duret 2007). Meiotic recombination between homologous chromosomes that are heterozygous at a particular locus can produce a DNA mismatch. DNA repair mechanisms are biased towards repairing a mismatch to the CG base pair. This will lead allele frequencies to change, leaving a signature of non-neutral evolution (Galtier et al. 2001). The excess of AT to GC mutations in human genomic regions with high substitution rates (human accelerated regions, HARs) implies that BGC has occurred frequently in the human genome (Pollard et al. 2006, Galtier and Duret 2007). Initially, it was postulated that BGC could have been adaptive (Galtier et al. 2001), but more recent observations have made this seem unlikely. Firstly, some HARs show no substantial signs of selective sweeps around them. Secondly, HARs tend to be present in regions with high recombination rates (Pollard et al. 2006). In fact, BGC could lead to HARs containing a high frequency of deleterious mutations (Galtier and Duret 2007). However, it is unlikely that HARs are generally maladaptive, because DNA repair mechanisms themselves would be subject to strong selection if they propagated deleterious mutations. Either way, BGC should be further investigated, because it may force radical alteration of the methods which test for the presence of adaptive evolution.

Adaptation

In biology, adaptation has three related meanings. Firstly, it is the dynamic evolutionary process that fits organisms to their environment, enhancing their evolutionary fitness. Secondly, it is a state reached by the population during that process. Thirdly, it is a phenotypic trait or adaptive trait, with a functional role in each individual organism, that is maintained and has evolved through natural selection.

Historically, adaptation has been described from the time of the ancient Greek philosophers such as Empedocles and Aristotle. In 18th and 19th century natural theology, adaptation was taken as evidence for the existence of a deity. Charles Darwin proposed instead that it was explained by natural selection.

Adaptation is related to biological fitness, which governs the rate of evolution as measured by change in gene frequencies. Often, two or more species co-adapt and co-evolve as they develop adaptations that interlock with those of the other species, such as with flowering plants and pollinating insects. In mimicry, species evolve to resemble other species; in Müllerian mimicry this is a mutually beneficial co-evolution as each of a group of strongly defended species (such as wasps able to sting) come to advertise their defences in the same way. Features evolved for one purpose may be co-opted for a different one, as when the insulating feathers of dinosaurs were co-opted for bird flight.

Adaptation is a major topic in the philosophy of biology, as it concerns function and purpose (teleology). Some biologists try to avoid terms which imply purpose in adaptation, not least because it suggests a deity's intentions, but others note that adaptation is necessarily purposeful.

History

Adaptation is an observable fact of life accepted by philosophers and natural historians from ancient times, independently of their views on evolution, but their explanations differed. Empedocles did not believe that adaptation required a final cause (a purpose), but thought that it "came about naturally, since such things survived." Aristotle did believe in final causes, but assumed that species were fixed.

The second of Jean-Baptiste Lamarck's two factors (the first being a complexifying force) was an adaptive force that causes animals with a given body plan to adapt to circumstances by inheritance of acquired characteristics, creating a diversity of species and genera.

In natural theology, adaptation was interpreted as the work of a deity and as evidence for the existence of God. William Paley believed that organisms were perfectly adapted to the lives they led, an argument that shadowed Gottfried Wilhelm Leibniz, who had argued that God had brought about "the best of all possible worlds." Voltaire's satire Dr. Pangloss is a parody of this optimistic idea, and David Hume also argued against design. The Bridgewater Treatises are a product of natural theology, though some of the authors managed to present their work in a fairly neutral manner. The series was lampooned by Robert Knox, who held quasi-evolutionary views, as the Bilgewater Treatises. Charles Darwin broke with the tradition by emphasising the flaws and limitations which occurred in the animal and plant worlds.

Jean-Baptiste Lamarck proposed a tendency for organisms to become more complex, moving up a ladder of progress, plus "the influence of circumstances," usually expressed as use and disuse. This second, subsidiary element of his theory is what is now called Lamarckism, a proto-evolutionary hypothesis of the inheritance of acquired characteristics, intended to explain adaptations by natural means.

Other natural historians, such as Buffon, accepted adaptation, and some also accepted evolution, without voicing their opinions as to the mechanism. This illustrates the real merit of Darwin and Alfred Russel Wallace, and secondary figures such as Henry Walter Bates, for putting forward a mechanism whose significance had only been glimpsed previously. A century later, experimental field studies and breeding experiments by people such as E. B. Ford and Theodosius Dobzhansky produced evidence that natural selection was not only the 'engine' behind adaptation, but was a much stronger force than had previously been thought.

General principles

The significance of an adaptation can only be understood in relation to the total biology of the species.

— Julian Huxley, Evolution: The Modern Synthesis

What adaptation is

Adaptation is primarily a process rather than a physical form or part of a body. An internal parasite (such as a liver fluke) can illustrate the distinction: such a parasite may have a very simple bodily structure, but nevertheless the organism is highly adapted to its specific environment. From this we see that adaptation is not just a matter of visible traits: in such parasites critical adaptations take place in the life cycle, which is often quite complex. However, as a practical term, "adaptation" often refers to a product: those features of a species which result from the process. Many aspects of an animal or plant can be correctly called adaptations, though there are always some features whose function remains in doubt. By using the term adaptation for the evolutionary process, and adaptive trait for the bodily part or function (the product), one may distinguish the two different senses of the word.

Adaptation is one of the two main processes that explain the observed diversity of species, such as the different species of Darwin's finches. The other process is speciation, in which new species arise, typically through reproductive isolation. An example widely used today to study the interplay of adaptation and speciation is the evolution of cichlid fish in African lakes, where the question of reproductive isolation is complex.

Adaptation is not always a simple matter where the ideal phenotype evolves for a given environment. An organism must be viable at all stages of its development and at all stages of its evolution. This places constraints on the evolution of development, behaviour, and structure of organisms. The main constraint, over which there has been much debate, is the requirement that each genetic and phenotypic change during evolution should be relatively small, because developmental systems are so complex and interlinked. However, it is not clear what "relatively small" should mean, for example polyploidy in plants is a reasonably common large genetic change. The origin of eukaryotic endosymbiosis is a more dramatic example.

All adaptations help organisms survive in their ecological niches. The adaptive traits may be structural, behavioural or physiological. Structural adaptations are physical features of an organism, such as shape, body covering, armament, and internal organization. Behavioural adaptations are inherited systems of behaviour, whether inherited in detail as instincts, or as a neuropsychological capacity for learning. Examples include searching for food, mating, and vocalizations. Physiological adaptations permit the organism to perform special functions such as making venom, secreting slime, and phototropism), but also involve more general functions such as growth and development, temperature regulation, ionic balance and other aspects of homeostasis. Adaptation affects all aspects of the life of an organism.

The following definitions are given by the evolutionary biologist Theodosius Dobzhansky:

1. Adaptation is the evolutionary process whereby an organism becomes better able to live in its habitat or habitats.

2. Adaptedness is the state of being adapted: the degree to which an organism is able to live and reproduce in a given set of habitats.

3. An adaptive trait is an aspect of the developmental pattern of the organism which enables or enhances the probability of that organism surviving and reproducing.

What adaptation is not

Some generalists, such as birds, have the flexibility to adapt to urban areas.

Adaptation differs from flexibility, acclimatization, and learning, all of which are changes during life which are not inherited. Flexibility deals with the relative capacity of an organism to maintain itself in different habitats: its degree of specialization. Acclimatization describes automatic physiological adjustments during life; learning means improvement in behavioural performance during life.

Flexibility stems from phenotypic plasticity, the ability of an organism with a given genotype (genetic type) to change its phenotype (observable characteristics) in response to changes in its habitat, or to move to a different habitat. The degree of flexibility is inherited, and varies between individuals. A highly specialized animal or plant lives only in a well-defined habitat, eats a specific type of food, and cannot survive if its needs are not met. Many herbivores are like this; extreme examples are koalas which depend on Eucalyptus, and giant pandas which require bamboo. A generalist, on the other hand, eats a range of food, and can survive in many different conditions. Examples are humans, rats, crabs and many carnivores. The tendency to behave in a specialized or exploratory manner is inherited—it is an adaptation. Rather different is developmental flexibility: "An animal or plant is developmentally flexible if when it is raised in or transferred to new conditions, it changes in structure so that it is better fitted to survive in the new environment," writes evolutionary biologist John Maynard Smith.

If humans move to a higher altitude, respiration and physical exertion become a problem, but after spending time in high altitude conditions they acclimatize to the reduced partial pressure of oxygen, such as by producing more red blood cells. The ability to acclimatize is an adaptation, but the acclimatization itself is not. The reproductive rate declines, but deaths from some tropical diseases also go down. Over a longer period of time, some people are better able to reproduce at high altitudes than others. They contribute more heavily to later generations, and gradually by natural selection the whole population becomes adapted to the new conditions. This has demonstrably occurred, as the observed performance of long-term communities at higher altitude is significantly better than the performance of new arrivals, even when the new arrivals have had time to acclimatize.

Adaptedness and fitness

There is a relationship between adaptedness and the concept of fitness used in population genetics. Differences in fitness between genotypes predict the rate of evolution by natural selection. Natural selection changes the relative frequencies of alternative phenotypes, insofar as they are heritable. However, a phenotype with high adaptedness may not have high fitness. Dobzhansky mentioned the example of the Californian redwood, which is highly adapted, but a relict species in danger of extinction. Elliott Sober commented that adaptation was a retrospective concept since it implied something about the history of a trait, whereas fitness predicts a trait's future.

1. Relative fitness. The average contribution to the next generation by a genotype or a class of genotypes, relative to the contributions of other genotypes in the population. This is also known as Darwinian fitness, selection coefficient, and other terms.

2. Absolute fitness. The absolute contribution to the next generation by a genotype or a class of genotypes. Also known as the Malthusian parameter when applied to the population as a whole.

3. Adaptedness. The extent to which a phenotype fits its local ecological niche. Researchers can sometimes test this through a reciprocal transplant.

In this sketch of a fitness landscape, a population can evolve by following the arrows to the adaptive peak at point B, and the points A and C are local optima where a population could become trapped.

Sewall Wright proposed that populations occupy adaptive peaks on a fitness landscape. To evolve to another, higher peak, a population would first have to pass through a valley of maladaptive intermediate stages, and might be "trapped" on a peak that is not optimally adapted.

Types

Adaptation is the heart and soul of evolution.

— Niles Eldredge, Reinventing Darwin: The Great Debate at the High Table of Evolutionary Theory

Changes in habitat

Before Darwin, adaptation was seen as a fixed relationship between an organism and its habitat. It was not appreciated that as the climate changed, so did the habitat; and as the habitat changed, so did the biota. Also, habitats are subject to changes in their biota: for example, invasions of species from other areas. The relative numbers of species in a given habitat are always changing. Change is the rule, though much depends on the speed and degree of the change. When the habitat changes, three main things may happen to a resident population: habitat tracking, genetic change or extinction. In fact, all three things may occur in sequence. Of these three effects only genetic change brings about adaptation. When a habitat changes, the resident population typically moves to more suitable places; this is the typical response of flying insects or oceanic organisms, which have wide (though not unlimited) opportunity for movement. This common response is called habitat tracking. It is one explanation put forward for the periods of apparent stasis in the fossil record (the punctuated equilibrium theory).

Genetic change

Genetic change occurs in a population when natural selection and mutations act on its genetic variability. The first pathways of enzyme-based metabolism may have been parts of purine nucleotide metabolism, with previous metabolic pathways being part of the ancient RNA world. By this means, the population adapts genetically to its circumstances. Genetic changes may result in visible structures, or may adjust physiological activity in a way that suits the habitat. The varying shapes of the beaks of Darwin's finches, for example, are driven by differences in the ALX1 gene.

Habitats and biota do frequently change. Therefore, it follows that the process of adaptation is never finally complete. Over time, it may happen that the environment changes little, and the species comes to fit its surroundings better and better. On the other hand, it may happen that changes in the environment occur relatively rapidly, and then the species becomes less and less well adapted. Seen like this, adaptation is a genetic tracking process, which goes on all the time to some extent, but especially when the population cannot or does not move to another, less hostile area. Given enough genetic change, as well as specific demographic conditions, an adaptation may be enough to bring a population back from the brink of extinction in a process called evolutionary rescue. Adaptation does affect, to some extent, every species in a particular ecosystem.

Leigh Van Valen thought that even in a stable environment, competing species constantly had to adapt to maintain their relative standing. This became known as the Red Queen hypothesis, as seen in host-parasite interaction.

Existing genetic variation and mutation were the traditional sources of material on which natural selection could act. In addition, horizontal gene transfer is possible between organisms in different species, using mechanisms as varied as gene cassettes, plasmids, transposons and viruses such as bacteriophages.

Co-adaptation

Pollinating insects are co-adapted with flowering plants.

In coevolution, where the existence of one species is tightly bound up with the life of another species, new or 'improved' adaptations which occur in one species are often followed by the appearance and spread of corresponding features in the other species. These co-adaptational relationships are intrinsically dynamic, and may continue on a trajectory for millions of years, as has occurred in the relationship between flowering plants and pollinating insects.

Mimicry

Images A and B show real wasps; the others show Batesian mimics: three hoverflies and one beetle.

Bates' work on Amazonian butterflies led him to develop the first scientific account of mimicry, especially the kind of mimicry which bears his name: Batesian mimicry. This is the mimicry by a palatable species of an unpalatable or noxious species (the model), gaining a selective advantage as predators avoid the model and therefore also the mimic. Mimicry is thus an anti-predator adaptation. A common example seen in temperate gardens is the hoverfly, many of which—though bearing no sting—mimic the warning coloration of hymenoptera (wasps and bees). Such mimicry does not need to be perfect to improve the survival of the palatable species.

Bates, Wallace and Fritz Müller believed that Batesian and Müllerian mimicry provided evidence for the action of natural selection, a view which is now standard amongst biologists.

Trade-offs

It is a profound truth that Nature does not know best; that genetical evolution... is a story of waste, makeshift, compromise and blunder.

— Peter Medawar, The Future of Man

All adaptations have a downside: horse legs are great for running on grass, but they can't scratch their backs; mammals' hair helps temperature, but offers a niche for ectoparasites; the only flying penguins do is under water. Adaptations serving different functions may be mutually destructive. Compromise and makeshift occur widely, not perfection. Selection pressures pull in different directions, and the adaptation that results is some kind of compromise.

Since the phenotype as a whole is the target of selection, it is impossible to improve simultaneously all aspects of the phenotype to the same degree.

— Ernst Mayr, The Growth of Biological Thought: Diversity, Evolution, and Inheritance

Consider the antlers of the Irish elk, (often supposed to be far too large; in deer antler size has an allometric relationship to body size). Obviously, antlers serve positively for defence against predators, and to score victories in the annual rut. But they are costly in terms of resource. Their size during the last glacial period presumably depended on the relative gain and loss of reproductive capacity in the population of elks during that time. As another example, camouflage to avoid detection is destroyed when vivid coloration is displayed at mating time. Here the risk to life is counterbalanced by the necessity for reproduction.

Stream-dwelling salamanders, such as Caucasian salamander or Gold-striped salamander have very slender, long bodies, perfectly adapted to life at the banks of fast small rivers and mountain brooks. Elongated body protects their larvae from being washed out by current. However, elongated body increases risk of desiccation and decreases dispersal ability of the salamanders; it also negatively affects their fecundity. As a result, fire salamander, less perfectly adapted to the mountain brook habitats, is in general more successful, have a higher fecundity and broader geographic range.

An Indian peacock's train
in full display

The peacock's ornamental train (grown anew in time for each mating season) is a famous adaptation. It must reduce his maneuverability and flight, and is hugely conspicuous; also, its growth costs food resources. Darwin's explanation of its advantage was in terms of sexual selection: "This depends on the advantage which certain individuals have over other individuals of the same sex and species, in exclusive relation to reproduction." The kind of sexual selection represented by the peacock is called 'mate choice,' with an implication that the process selects the more fit over the less fit, and so has survival value. The recognition of sexual selection was for a long time in abeyance, but has been rehabilitated.

The conflict between the size of the human foetal brain at birth, (which cannot be larger than about 400 cm³, else it will not get through the mother's pelvis) and the size needed for an adult brain (about 1400 cm³), means the brain of a newborn child is quite immature. The most vital things in human life (locomotion, speech) just have to wait while the brain grows and matures. That is the result of the birth compromise. Much of the problem comes from our upright bipedal stance, without which our pelvis could be shaped more suitably for birth. Neanderthals had a similar problem.

As another example, the long neck of a giraffe brings benefits but at a cost. The neck of a giraffe can be up to 2 m (6 ft 7 in) in length. The benefits are that it can be used for inter-species competition or for foraging on tall trees where shorter herbivores cannot reach. The cost is that a long neck is heavy and adds to the animal's body mass, requiring additional energy to build the neck and to carry its weight around.

Shifts in function

Adaptation and function are two aspects of one problem

— Julian Huxley, Evolution: The Modern Synthesis

Pre-adaptation

Pre-adaptation occurs when a population has characteristics which by chance are suited for a set of conditions not previously experienced. For example, the polyploid cordgrass Spartina townsendii is better adapted than either of its parent species to their own habitat of saline marsh and mud-flats. Among domestic animals, the White Leghorn chicken is markedly more resistant to vitamin B₁ deficiency than other breeds; on a plentiful diet this makes no difference, but on a restricted diet this preadaptation could be decisive.

Pre-adaptation may arise because a natural population carries a huge quantity of genetic variability. In diploid eukaryotes, this is a consequence of the system of sexual reproduction, where mutant alleles get partially shielded, for example, by genetic dominance. Microorganisms, with their huge populations, also carry a great deal of genetic variability. The first experimental evidence of the pre-adaptive nature of genetic variants in microorganisms was provided by Salvador Luria and Max Delbrück who developed the Fluctuation Test, a method to show the random fluctuation of pre-existing genetic changes that conferred resistance to bacteriophages in Escherichia coli.

Co-option of existing traits: exaptation

The feathers of Sinosauropteryx, a dinosaur with feathers, were used for insulation, making them an exaptation for flight.

Features that now appear as adaptations sometimes arose by co-option of existing traits, evolved for some other purpose. The classic example is the ear ossicles of mammals, which we know from paleontological and embryological evidence originated in the upper and lower jaws and the hyoid bone of their synapsid ancestors, and further back still were part of the gill arches of early fish. The word exaptation was coined to cover these common evolutionary shifts in function. The flight feathers of birds evolved from the much earlier feathers of dinosaurs, which might have been used for insulation or for display.

Niche construction

Animals including earthworms, beavers and humans use some of their adaptations to modify their surroundings, so as to maximize their chances of surviving and reproducing. Beavers create dams and lodges, changing the ecosystems of the valleys around them. Earthworms, as Darwin noted, improve the topsoil in which they live by incorporating organic matter. Humans have constructed extensive civilizations with cities in environments as varied as the Arctic and hot deserts. In all three cases, the construction and maintenance of ecological niches helps drive the continued selection of the genes of these animals, in an environment that the animals have modified.

Non-adaptive traits

Some traits do not appear to be adaptive as they have a neutral or deleterious effect on fitness in the current environment. Because genes often have pleiotropic effects, not all traits may be functional: they may be what Stephen Jay Gould and Richard Lewontin called spandrels, features brought about by neighbouring adaptations, on the analogy with the often highly decorated triangular areas between pairs of arches in architecture, which began as functionless features.

Another possibility is that a trait may have been adaptive at some point in an organism's evolutionary history, but a change in habitats caused what used to be an adaptation to become unnecessary or even maladapted. Such adaptations are termed vestigial. Many organisms have vestigial organs, which are the remnants of fully functional structures in their ancestors. As a result of changes in lifestyle the organs became redundant, and are either not functional or reduced in functionality. Since any structure represents some kind of cost to the general economy of the body, an advantage may accrue from their elimination once they are not functional. Examples: wisdom teeth in humans; the loss of pigment and functional eyes in cave fauna; the loss of structure in endoparasites.

Extinction and coextinction

If a population cannot move or change sufficiently to preserve its long-term viability, then obviously, it will become extinct, at least in that locale. The species may or may not survive in other locales. Species extinction occurs when the death rate over the entire species exceeds the birth rate for a long enough period for the species to disappear. It was an observation of Van Valen that groups of species tend to have a characteristic and fairly regular rate of extinction.

Just as there is co-adaptation, there is also coextinction, the loss of a species due to the extinction of another with which it is coadapted, as with the extinction of a parasitic insect following the loss of its host, or when a flowering plant loses its pollinator, or when a food chain is disrupted.

Philosophical issues

"Behaviour with a purpose": a young springbok stotting. A biologist might argue that this has the function of signalling to predators, helping the springbok to survive and allowing it to reproduce.

Adaptation raises philosophical issues concerning how biologists speak of function and purpose, as this carries implications of evolutionary history – that a feature evolved by natural selection for a specific reason – and potentially of supernatural intervention – that features and organisms exist because of a deity's conscious intentions. In his biology, Aristotle introduced teleology to describe the adaptedness of organisms, but without accepting the supernatural intention built into Plato's thinking, which Aristotle rejected. Modern biologists continue to face the same difficulty. On the one hand, adaptation is obviously purposeful: natural selection chooses what works and eliminates what does not. On the other hand, biologists by and large reject conscious purpose in evolution. The dilemma gave rise to a famous joke by the evolutionary biologist Haldane: "Teleology is like a mistress to a biologist: he cannot live without her but he's unwilling to be seen with her in public.'" David Hull commented that Haldane's mistress "has become a lawfully wedded wife. Biologists no longer feel obligated to apologize for their use of teleological language; they flaunt it." Ernst Mayr stated that "adaptedness... is a posteriori result rather than an a priori goal-seeking", meaning that the question of whether something is an adaptation can only be determined after the event.